Nature Chemical Biology Contents: June 2012 Volume 8 Number 6, pp 495 - 596

Advertisement High Impact Biological Chemistry RSC Publishing Biology Journals are creating a new paradigm in biology by addressing real problems and real scientific issues of concern in today's world www.rsc.org/BiologicalPort TABLE OF CONTENTS June 2012 Volume 8, Issue 6 Focus Editorial Commentary Research Highlights News and Views Reviews Articles Advertisement Looking to keep pace with global news and research in the chemical sciences? Join RSC e-membership today to receive a digital subscription to Chemistry World, the unrivalled monthly magazine with an international readership of 49,000 scientists. Access the latest developments in research and government policy, business news, features and opinion columns, jobs board, and networking opportunities. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement The nature.com open innovation pavilion now has several research and development Challenges in genetics, molecular cell biology, chemistry, physics, immunology and more! Submit your solution to any of our Challenges for a chance to win cash awards ranging from $5,000 to $1M. Visit the pavilion or become a Solver today!   Focus Top Metabolism in 3D Metabolism is reemerging as a central topic in chemistry and biology, and chemical biologists are poised to improve our understanding of complex questions such as regulation, flux, and spatial organization. In this issue, we feature reviews and commentary outlining the recent advances and outstanding challenges in metabolism research. Metabolism in 3D Editorial Top Beyond blueprints p495 doi:10.1038/nchembio.997 Renewed interest in the biological significance and applied outcomes of metabolism is moving the field from static biochemical charts to multidimensional networks. Full Text | PDF Commentary Top Teaching the design principles of metabolism pp497 - 501 Joshua D Rabinowitz and Livia Vastag doi:10.1038/nchembio.969 Learning metabolism inevitably involves memorizing pathways. The teacher's challenge is to motivate memorization and to help students progress beyond it. To this end, students should be taught a few fundamental chemical reaction mechanisms and how these are repeatedly used to achieve pathway goals. Pathway knowledge should then be reinforced through quantitative problems that emphasize the relevance of metabolism to bioengineering and medicine. Full Text | PDF Research Highlights Top Metabolic engineering: Assembling activity | RNA transport: An hnRNP ruler | Stem cells: Imatinib gets beta | Neurobiology: Smells like mitochondria | Chemical probes: Motor control | Metabolism: Lathosterone for longer life | Biosynthesis: Malonyl? Stet. | Cell biology: Peroxisomes come together News and Views Top Structural biology: CrkL is not Crk-like pp504 - 505 Yoshihiro Kobashigawa and Fuyuhiko Inagaki doi:10.1038/nchembio.963 Crk-like (CrkL) is a key signaling protein that mediates the leukemogenic activity of Bcr-Abl. Structural investigations show that the intramolecular assembly of CrkL is entirely distinct from that of CrkII, shedding light on how CrkL specifically mediates Bcr-Abl signaling. Full Text | PDF See also: Article by Jankowski et al. Biosynthesis: Ringing in a new view pp505 - 507 Wendy L Kelly doi:10.1038/nchembio.973 Heterocycles such as thiazoles are introduced into ribosomally synthesized peptide metabolites by post-translational modification. The enzyme that installs those rings has been identified, providing insight into heterocyclization biochemistry and the potential capabilities of an entire protein family. Full Text | PDF See also: Article by Dunbar et al. Antisense therapeutics: New ways to nudge splicing pp507 - 508 Ian Eperon doi:10.1038/nchembio.968 Duplexes formed between pre-mRNA and 2′-fluorinated oligonucleotides suppress nearby splice sites by recruiting double-stranded RNA-binding proteins. Full Text | PDF See also: Article by Rigo et al. Chemical Biology JOBS of the week Chemical synthesis of nanostructures Scuola Normale Superiore di Pisa Postdoctoral Fellowship – Chemical Biology Division New England Biolabs, Inc. ETH Zurich PhD in Chemical Toxicology ETH Zurich (Swiss Federal Institute of Technology) Postdoctoral Position in Chemical Modification of Antibodies Institute for Research in Biomedicine (IRB Barcelona) Chemical Engineer 1937 Merck Millipore Ltd., Ire More Science jobs from Chemical Biology EVENT International Conference on Bioinspired and Biobased Chemistry & Materials 3-5 October 2012 Nice, France More science events from Reviews Top Rethinking glycolysis: on the biochemical logic of metabolic pathways pp509 - 517 Arren Bar-Even, Avi Flamholz, Elad Noor and Ron Milo doi:10.1038/nchembio.971 Abstract | Full Text | PDF Engineering synthetic recursive pathways to generate non-natural small molecules pp518 - 526 Elizabeth A Felnagle, Asha Chaubey, Elizabeth L Noey, Kendall N Houk and James C Liao doi:10.1038/nchembio.959 Abstract | Full Text | PDF Natural strategies for the spatial optimization of metabolism in synthetic biology pp527 - 535 Christina M Agapakis, Patrick M Boyle and Pamela A Silver doi:10.1038/nchembio.975 Abstract | Full Text | PDF Systems metabolic engineering of microorganisms for natural and non-natural chemicals pp536 - 546 Jeong Wook Lee, Dokyun Na, Jong Myoung Park, Joungmin Lee, Sol Choi and Sang Yup Lee doi:10.1038/nchembio.970 Abstract | Full Text | PDF Articles Top Trp-tRNA synthetase bridges DNA-PKcs to PARP-1 to link IFN-γ and p53 signaling pp547 - 554 Mathew Sajish, Quansheng Zhou, Shuji Kishi, Delgado M Valdez Jr, Mili Kapoor, Min Guo, Sunhee Lee, Sunghoon Kim, Xiang-Lei Yang and Paul Schimmel doi:10.1038/nchembio.937 Trp-tRNA synthetase (TrpRS) has a well-understood role in translation by facilitating aminoacylation of Trp-tRNAs. The discovery of a nuclear signaling role for TrpRS as a bridging protein for DNA-PK and PARP-1, resulting in p53 activation, explains a previously curious link between interferon-γ signaling and concomitant TrpRS overexpression. Abstract | Full Text | PDF Synthetic oligonucleotides recruit ILF2/3 to RNA transcripts to modulate splicing pp555 - 561 Frank Rigo, Yimin Hua, Seung J Chun, Thazha P Prakash, Adrian R Krainer and C Frank Bennett doi:10.1038/nchembio.939 Antisense oligonucleotides (ASOs) are widely used to modulate gene expression through sequence-specific duplex formation with target RNAs. ASOs containing specific 2′-fluorine substitutions are shown to recruit ILF2/3 to pre-mRNA and induce exon skipping in cells and in mice. Abstract | Full Text | PDF See also: News and Views by Eperon Ultrasensitive regulation of anapleurosis via allosteric activation of PEP carboxylase  pp562 - 568 Yi-Fan Xu, Daniel Amador-Noguez, Marshall Louis Reaves, Xiao-Jiang Feng and Joshua D Rabinowitz doi:10.1038/nchembio.941 Bacteria must control their metabolism to quickly adapt to changing carbon sources. PEP carboxylase is now shown to be allosterically regulated by fructose-1,6-bisphosphate in an ultrasensitive manner, turning glycolysis on and off almost instantaneously in response to glucose availability. Abstract | Full Text | PDF YcaO domains use ATP to activate amide backbones during peptide cyclodehydrations pp569 - 575 Kyle L Dunbar, Joel O Melby and Douglas A Mitchell doi:10.1038/nchembio.944 Cyclodehydrations in thiazole/oxazole-modified microcin biosynthesis are known to require a multiprotein complex, but full details of the reaction were not clear. Substrate analogs and isotopic labeling now show the D protein, thought to serve a scaffolding function, catalyzes ring formation and uses ATP to activate the substrate. Abstract | Full Text | PDF See also: News and Views by Kelly A selective inhibitor reveals PI3Kγ dependence of TH17 cell differentiation pp576 - 582 Giovanna Bergamini, Kathryn Bell, Satoko Shimamura, Thilo Werner, Andrew Cansfield, Katrin Müller, Jessica Perrin, Christina Rau, Katie Ellard, Carsten Hopf, Carola Doce, Daniel Leggate, Raffaella Mangano, Toby Mathieson, Alison O'Mahony, Ivan Plavec, Faiza Rharbaoui, Friedrich Reinhard, Mikhail M Savitski, Nigel Ramsden, Emilio Hirsch, Gerard Drewes, Oliver Rausch, Marcus Bantscheff and Gitte Neubauer doi:10.1038/nchembio.957 A chemoproteomic approach adapted for high-throughput screening leads to the identification of a selective PI3Kγ inhibitor. Application of this inhibitor in human and mouse cellular models reveals a role for PI3Kγ in TH17 cell differentiation. Abstract | Full Text | PDF | Chemical compounds Fluorescent castasterone reveals BRI1 signaling from the plasma membrane pp583 - 589 Niloufer G Irani, Simone Di Rubbo, Evelien Mylle, Jos Van den Begin, Joanna Schneider-Pizoń, Jaroslava Hniliková, Miroslav Šíša, Dieter Buyst, Josep Vilarrasa-Blasi, Anna-Mária Szatmári, Daniël Van Damme, Kiril Mishev, Mirela-Corina Codreanu, Ladislav Kohout, Miroslav Strnad, Ana I Caño-Delgado, Jiří Friml, Annemieke Madder and Eugenia Russinova doi:10.1038/nchembio.958 Brassinosteroids (BRs) are plant growth hormones that bind the brassinosteroid receptor (BRI1) and activate its kinase domain. Exploration of BRI1-BR trafficking using a fluorescent brassinosteroid probe alongside chemical and genetic tools reveals that endocytosis pathways are essential for BR signaling attenuation and BRI1 turnover. Abstract | Full Text | PDF | Chemical compounds Domain organization differences explain Bcr-Abl's preference for CrkL over CrkII  pp590 - 596 Wojciech Jankowski, Tamjeed Saleh, Ming-Tao Pai, Ganapathy Sriram, Raymond B Birge and Charalampos G Kalodimos doi:10.1038/nchembio.954 NMR structures of CrkL, an adaptor protein that mediates Bcr-Abl signaling in CML, reveal domain organization distinct from CrkII that allows constitutive interaction between CrkL and Abl kinase. Abstract | Full Text | PDF See also: News and Views by Kobashigawa & Inagaki Top Advertisement Nature.com presents Antibodypedia Finding the right antibody for the right application just got easier! Visit www.antibodypedia.com to find antibodies that have proved themselves effective for particular applications or to submit antibody validation data from your own experiments.   Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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